Sun 23 Dec 22:22:42 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hh6-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hh6-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.2-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.2-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:51 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hh6-3.2-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 198 and 0 Target number of residues in the AU: 198 Target solvent content: 0.6321 Checking the provided sequence file Detected sequence length: 113 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 226 Adjusted target solvent content: 0.58 Input MTZ file: 2hh6-3.2-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 179 Cell parameters: 93.536 93.536 115.318 90.000 90.000 120.000 Input sequence file: 2hh6-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1808 target number of atoms Had to go as low as 0.50 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 81.005 3.201 Wilson plot Bfac: 67.38 5291 reflections ( 99.68 % complete ) and 0 restraints for refining 2007 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3221 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3204 (Rfree = 0.000) for 2007 atoms. Found 17 (17 requested) and removed 34 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.13 2.81 Search for helices and strands: 0 residues in 0 chains, 2001 seeds are put forward NCS extension: 0 residues added, 2001 seeds are put forward Round 1: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.329 Round 2: 83 peptides, 14 chains. Longest chain 12 peptides. Score 0.352 Round 3: 99 peptides, 10 chains. Longest chain 27 peptides. Score 0.539 Round 4: 111 peptides, 11 chains. Longest chain 15 peptides. Score 0.572 Round 5: 111 peptides, 11 chains. Longest chain 21 peptides. Score 0.572 Taking the results from Round 5 Chains 13, Residues 100, Estimated correctness of the model 33.2 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 3198 restraints for refining 1548 atoms. 2668 conditional restraints added. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2931 (Rfree = 0.000) for 1548 atoms. Found 13 (13 requested) and removed 27 (6 requested) atoms. Cycle 2: After refmac, R = 0.2953 (Rfree = 0.000) for 1470 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 3: After refmac, R = 0.3068 (Rfree = 0.000) for 1424 atoms. Found 13 (13 requested) and removed 15 (6 requested) atoms. Cycle 4: After refmac, R = 0.2998 (Rfree = 0.000) for 1400 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 5: After refmac, R = 0.3045 (Rfree = 0.000) for 1377 atoms. Found 10 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 2.89 Search for helices and strands: 0 residues in 0 chains, 1404 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 1421 seeds are put forward Round 1: 96 peptides, 12 chains. Longest chain 17 peptides. Score 0.477 Round 2: 116 peptides, 12 chains. Longest chain 22 peptides. Score 0.573 Round 3: 113 peptides, 13 chains. Longest chain 24 peptides. Score 0.538 Round 4: 105 peptides, 13 chains. Longest chain 19 peptides. Score 0.499 Round 5: 108 peptides, 15 chains. Longest chain 25 peptides. Score 0.467 Taking the results from Round 2 Chains 12, Residues 104, Estimated correctness of the model 33.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2688 restraints for refining 1308 atoms. 2284 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3038 (Rfree = 0.000) for 1308 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 7: After refmac, R = 0.2804 (Rfree = 0.000) for 1279 atoms. Found 11 (11 requested) and removed 21 (5 requested) atoms. Cycle 8: After refmac, R = 0.2489 (Rfree = 0.000) for 1261 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 1256 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 10: After refmac, R = 0.2301 (Rfree = 0.000) for 1250 atoms. Found 10 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 2.87 Search for helices and strands: 0 residues in 0 chains, 1300 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 1323 seeds are put forward Round 1: 99 peptides, 12 chains. Longest chain 23 peptides. Score 0.492 Round 2: 106 peptides, 10 chains. Longest chain 28 peptides. Score 0.572 Round 3: 104 peptides, 9 chains. Longest chain 33 peptides. Score 0.585 Round 4: 105 peptides, 10 chains. Longest chain 24 peptides. Score 0.567 Round 5: 108 peptides, 10 chains. Longest chain 30 peptides. Score 0.581 Taking the results from Round 3 Chains 12, Residues 95, Estimated correctness of the model 36.9 % 2 chains (44 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2329 restraints for refining 1334 atoms. 1761 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2752 (Rfree = 0.000) for 1334 atoms. Found 11 (11 requested) and removed 26 (5 requested) atoms. Cycle 12: After refmac, R = 0.2675 (Rfree = 0.000) for 1302 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 13: After refmac, R = 0.2626 (Rfree = 0.000) for 1282 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 14: After refmac, R = 0.2599 (Rfree = 0.000) for 1269 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 15: After refmac, R = 0.2593 (Rfree = 0.000) for 1261 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.86 Search for helices and strands: 0 residues in 0 chains, 1286 seeds are put forward NCS extension: 0 residues added, 1286 seeds are put forward Round 1: 93 peptides, 12 chains. Longest chain 22 peptides. Score 0.461 Round 2: 106 peptides, 14 chains. Longest chain 16 peptides. Score 0.481 Round 3: 92 peptides, 11 chains. Longest chain 21 peptides. Score 0.480 Round 4: 90 peptides, 11 chains. Longest chain 20 peptides. Score 0.470 Round 5: 99 peptides, 9 chains. Longest chain 36 peptides. Score 0.562 Taking the results from Round 5 Chains 12, Residues 90, Estimated correctness of the model 30.3 % 4 chains (47 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2559 restraints for refining 1396 atoms. 2008 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2826 (Rfree = 0.000) for 1396 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 17: After refmac, R = 0.2833 (Rfree = 0.000) for 1383 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.2847 (Rfree = 0.000) for 1370 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 19: After refmac, R = 0.2940 (Rfree = 0.000) for 1357 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 20: After refmac, R = 0.2945 (Rfree = 0.000) for 1348 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1375 seeds are put forward NCS extension: 0 residues added, 1375 seeds are put forward Round 1: 93 peptides, 12 chains. Longest chain 23 peptides. Score 0.461 Round 2: 95 peptides, 11 chains. Longest chain 24 peptides. Score 0.496 Round 3: 89 peptides, 11 chains. Longest chain 18 peptides. Score 0.465 Round 4: 101 peptides, 11 chains. Longest chain 24 peptides. Score 0.526 Round 5: 94 peptides, 8 chains. Longest chain 23 peptides. Score 0.562 Taking the results from Round 5 Chains 9, Residues 86, Estimated correctness of the model 30.3 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2868 restraints for refining 1379 atoms. 2457 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2423 (Rfree = 0.000) for 1379 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 22: After refmac, R = 0.2461 (Rfree = 0.000) for 1369 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 23: After refmac, R = 0.2894 (Rfree = 0.000) for 1358 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 24: After refmac, R = 0.2389 (Rfree = 0.000) for 1334 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2365 (Rfree = 0.000) for 1329 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.85 Search for helices and strands: 0 residues in 0 chains, 1361 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 1374 seeds are put forward Round 1: 83 peptides, 11 chains. Longest chain 15 peptides. Score 0.432 Round 2: 90 peptides, 10 chains. Longest chain 21 peptides. Score 0.495 Round 3: 91 peptides, 12 chains. Longest chain 18 peptides. Score 0.450 Round 4: 97 peptides, 11 chains. Longest chain 24 peptides. Score 0.506 Round 5: 100 peptides, 12 chains. Longest chain 27 peptides. Score 0.497 Taking the results from Round 4 Chains 12, Residues 86, Estimated correctness of the model 13.2 % 1 chains (22 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2743 restraints for refining 1370 atoms. 2330 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3053 (Rfree = 0.000) for 1370 atoms. Found 12 (12 requested) and removed 24 (6 requested) atoms. Cycle 27: After refmac, R = 0.2901 (Rfree = 0.000) for 1339 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. Cycle 28: After refmac, R = 0.2767 (Rfree = 0.000) for 1336 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 29: After refmac, R = 0.2774 (Rfree = 0.000) for 1331 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2810 (Rfree = 0.000) for 1327 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1354 seeds are put forward NCS extension: 9 residues added (1 deleted due to clashes), 1363 seeds are put forward Round 1: 88 peptides, 11 chains. Longest chain 27 peptides. Score 0.459 Round 2: 94 peptides, 12 chains. Longest chain 19 peptides. Score 0.466 Round 3: 99 peptides, 15 chains. Longest chain 19 peptides. Score 0.419 Round 4: 92 peptides, 15 chains. Longest chain 12 peptides. Score 0.379 Round 5: 98 peptides, 14 chains. Longest chain 16 peptides. Score 0.438 Taking the results from Round 2 Chains 12, Residues 82, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2771 restraints for refining 1360 atoms. 2416 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2733 (Rfree = 0.000) for 1360 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 32: After refmac, R = 0.2872 (Rfree = 0.000) for 1341 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 33: After refmac, R = 0.2792 (Rfree = 0.000) for 1322 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 34: After refmac, R = 0.2750 (Rfree = 0.000) for 1318 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 35: After refmac, R = 0.2768 (Rfree = 0.000) for 1302 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1352 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 1378 seeds are put forward Round 1: 78 peptides, 12 chains. Longest chain 11 peptides. Score 0.376 Round 2: 107 peptides, 15 chains. Longest chain 15 peptides. Score 0.462 Round 3: 116 peptides, 18 chains. Longest chain 21 peptides. Score 0.439 Round 4: 105 peptides, 16 chains. Longest chain 15 peptides. Score 0.428 Round 5: 110 peptides, 16 chains. Longest chain 20 peptides. Score 0.454 Taking the results from Round 2 Chains 15, Residues 92, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2716 restraints for refining 1355 atoms. 2281 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2365 (Rfree = 0.000) for 1355 atoms. Found 10 (12 requested) and removed 12 (6 requested) atoms. Cycle 37: After refmac, R = 0.2770 (Rfree = 0.000) for 1350 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 38: After refmac, R = 0.2916 (Rfree = 0.000) for 1336 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 39: After refmac, R = 0.2799 (Rfree = 0.000) for 1326 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. Cycle 40: After refmac, R = 0.2399 (Rfree = 0.000) for 1324 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 2.88 Search for helices and strands: 0 residues in 0 chains, 1369 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 1377 seeds are put forward Round 1: 92 peptides, 13 chains. Longest chain 10 peptides. Score 0.430 Round 2: 97 peptides, 12 chains. Longest chain 21 peptides. Score 0.482 Round 3: 96 peptides, 10 chains. Longest chain 16 peptides. Score 0.525 Round 4: 100 peptides, 12 chains. Longest chain 19 peptides. Score 0.497 Round 5: 100 peptides, 11 chains. Longest chain 19 peptides. Score 0.521 Taking the results from Round 3 Chains 11, Residues 86, Estimated correctness of the model 19.2 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 5291 reflections ( 99.68 % complete ) and 2629 restraints for refining 1348 atoms. 2184 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2607 (Rfree = 0.000) for 1348 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 42: After refmac, R = 0.2650 (Rfree = 0.000) for 1334 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 43: After refmac, R = 0.2557 (Rfree = 0.000) for 1326 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1918 (Rfree = 0.000) for 1323 atoms. Found 4 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.1813 (Rfree = 0.000) for 1318 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.86 Search for helices and strands: 0 residues in 0 chains, 1351 seeds are put forward NCS extension: 0 residues added, 1351 seeds are put forward Round 1: 88 peptides, 12 chains. Longest chain 15 peptides. Score 0.434 Round 2: 99 peptides, 13 chains. Longest chain 16 peptides. Score 0.468 Round 3: 96 peptides, 11 chains. Longest chain 21 peptides. Score 0.501 Round 4: 99 peptides, 12 chains. Longest chain 15 peptides. Score 0.492 Round 5: 99 peptides, 11 chains. Longest chain 17 peptides. Score 0.516 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 88, Estimated correctness of the model 16.4 % 1 chains (14 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2hh6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5291 reflections ( 99.68 % complete ) and 2708 restraints for refining 1370 atoms. 2305 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2573 (Rfree = 0.000) for 1370 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2721 (Rfree = 0.000) for 1356 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2807 (Rfree = 0.000) for 1347 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2716 (Rfree = 0.000) for 1340 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... TimeTaking 45.62